GSE129611 dataset

Sample GSM3717036

The goal of this script is to generate a Seurat object for sample GSM3717036.

• removal of cells based on quality control metrics
• normalization with LogNormalize, for only the remaining cells
• cell cycle and cell type annotation
• dimensionality reduction using PCA to obtain 50 dimensions
• projection using UMAP

We do not perform doublet detection in this dataset.

library(dplyr)
library(patchwork)
library(ggplot2)

.libPaths()

## [1] "/usr/local/lib/R/library"

Preparation

In this section, we set the global settings of the analysis. We will store data there :

out_dir = "."

We load the parameters :

sample_name = params$sample_name

Input count matrix is there :

count_matrix_dir = paste0(out_dir, "/input/", sample_name, "/")
count_matrix_file = list.files(count_matrix_dir, full.names = TRUE)
count_matrix_file

## [1] "./input/GSM3717036//GSM3717036_DS3-Rie_6_comb_clean.dge.txt.gz"

We load the markers and specific colors for each cell type :

cell_markers = readRDS(paste0(out_dir, "/../../1_metadata/hs_hd_cell_markers.rds"))
cell_markers = lapply(cell_markers, FUN = toupper)
lengths(cell_markers)

##          CD4 T cells          CD8 T cells     Langerhans cells 
##                   13                   13                    9 
##          macrophages              B cells              cuticle 
##                   10                   16                   15 
##               cortex              medulla                  IRS 
##                   16                   10                   16 
##        proliferative               HF-SCs            IFE basal 
##                   20                   17                   16 
## IFE granular spinous                  ORS          melanocytes 
##                   17                   15                   10 
##            sebocytes 
##                    8

Here are custom colors for each cell type :

color_markers = readRDS(paste0(out_dir, "/../../1_metadata/hs_hd_color_markers.rds"))

data.frame(cell_type = names(color_markers),
           color = unlist(color_markers)) %>%
  ggplot2::ggplot(., aes(x = cell_type, y = 0, fill = cell_type)) +
  ggplot2::geom_point(pch = 21, size = 5) +
  ggplot2::scale_fill_manual(values = unlist(color_markers), breaks = names(color_markers)) +
  ggplot2::theme_classic() +
  ggplot2::theme(legend.position = "none",
                 axis.line = element_blank(),
                 axis.title = element_blank(),
                 axis.ticks = element_blank(),
                 axis.text.y = element_blank())

We load markers to display on the dotplot :

dotplot_markers = readRDS(paste0(out_dir, "/../../1_metadata/hs_hd_dotplot_markers.rds"))
dotplot_markers = lapply(dotplot_markers, FUN = toupper)
dotplot_markers

## $`CD4 T cells`
## [1] "PTPRC" "CD3E"  "CD4"  
## 
## $`CD8 T cells`
## [1] "CD3E" "CD8A"
## 
## $`Langerhans cells`
## [1] "CD207" "CPVL" 
## 
## $macrophages
## [1] "TREM2" "MSR1" 
## 
## $`B cells`
## [1] "CD79A" "CD79B"
## 
## $cuticle
## [1] "MSX2"  "KRT32" "KRT35"
## 
## $cortex
## [1] "KRT31" "PRR9" 
## 
## $medulla
## [1] "BAMBI"   "ADLH1A3"
## 
## $IRS
## [1] "KRT71" "KRT73"
## 
## $proliferative
## [1] "TOP2A" "MCM5"  "TK1"  
## 
## $`HF-SCs`
## [1] "KRT14"  "CXCL14"
## 
## $`IFE basal`
## [1] "COL17A1" "KRT15"  
## 
## $`IFE granular spinous`
## [1] "SPINK5" "KRT1"  
## 
## $ORS
## [1] "KRT16" "KRT6C"
## 
## $melanocytes
## [1] "DCT"   "MLANA"
## 
## $sebocytes
## [1] "CLMP"  "PPARG"

We load metadata for this sample :

sample_info = readRDS(paste0(out_dir, "/../1_metadata/takahashi_sample_info.rds"))
sample_info %>%
  dplyr::filter(project_name == sample_name)

##   project_name sample_type sample_identifier platform gender   location
## 1   GSM3717036          HD    Takahashi_HD_3 Drop-Seq      M hair scalp
##   laboratory       color
## 1  Takahashi yellowgreen

We load the correspondence between gene names and Ensembl ID :

gene_corresp = readRDS(paste0(out_dir, "/../1_metadata/takahashi_gene_corresp.rds"))
head(gene_corresp)

##           gene_id  gene_name
## 1 ENSG00000223972    DDX11L1
## 2 ENSG00000227232     WASH7P
## 3 ENSG00000243485 MIR1302-11
## 4 ENSG00000237613    FAM138A
## 5 ENSG00000268020     OR4G4P
## 6 ENSG00000240361    OR4G11P

These is a parameter for different functions :

cl = aquarius::create_parallel_instance(nthreads = 3L)
cut_log_nCount_RNA = 0.5  # almost no filter
cut_nFeature_RNA = 250    # as in the publication
cut_percent.mt = 20
cut_percent.rb = 50

Load count matrix

In this section, we load the count matrix.

mat = read.table(count_matrix_file,
                 header = TRUE, row.names = 1)

# For the two 10X data, we remove the prefix
rownames(mat) = stringr::str_remove(rownames(mat),
                                    pattern = "hg19_")

mat[c(1:5), c(1:5)]

##          ACCGTTCACTAC CTAATAGTTTGA ATAGCATGCACC AGCCCCATTTAG GCAGTCTACCAT
## A1BG-AS1            0            0            0            0            0
## A2M                 0            0            0            0            0
## AAAS                0            0            0            0            0
## AACS                0            0            0            0            0
## AADAC               0            0            0            0            0

(Time to run : 20.4 s)

In genes metadata, we add the Ensembl ID. The sobj@assays$RNA@meta.features dataframe contains three information :

• Ensembl_ID : EnsemblID, as stored in the gene_corresp table
• gene_name : gene_name, as stored in the count matrix file. Duplicated gene names will have the same name.

How many genes are in common between the count matrix and the correspondence table ?

ggvenn::ggvenn(list(count_matrix = rownames(mat),
                    annotation = gene_corresp$gene_name), 
               fill_color = c("#0073C2FF", "#EFC000FF"),
               stroke_size = 0.5, set_name_size = 4) +
  ggplot2::ggtitle(label = "Gene names") +
  ggplot2::theme(plot.title = element_text(hjust = 0.5, face = "bold"))

We keep the intersection :

common_genes = intersect(rownames(mat), gene_corresp$gene_name)

length(common_genes)

## [1] 14170

length(unique(common_genes))

## [1] 14170

We define the same order for rownames in the matrix and gene name in the table

# Subset genes in gene_corresp
gene_corresp = gene_corresp %>%
  dplyr::filter(!duplicated(gene_name)) %>%
  dplyr::filter(gene_name %in% common_genes) %>%
  `rownames<-`(.$gene_name) %>%
  `colnames<-`(c("Ensembl_ID", "gene_name"))
gene_corresp = gene_corresp[common_genes, ]

# Subset genes in the matrix
mat = mat[common_genes, ]

# Genes are in the same order
all.equal(gene_corresp$gene_name, rownames(mat))

## [1] TRUE

We create a Seurat object with the genes for which Ensembl ID are available:

sobj = Seurat::CreateSeuratObject(counts = mat,
                                  project = sample_name,
                                  assay = "RNA")
sobj

## An object of class Seurat 
## 14170 features across 3000 samples within 1 assay 
## Active assay: RNA (14170 features, 0 variable features)

We add the correspondence in the Seurat object :

sobj@assays$RNA@meta.features = gene_corresp
rm(gene_corresp)

head(sobj@assays$RNA@meta.features)

##               Ensembl_ID gene_name
## A1BG-AS1 ENSG00000268895  A1BG-AS1
## A2M      ENSG00000175899       A2M
## AAAS     ENSG00000094914      AAAS
## AACS     ENSG00000081760      AACS
## AADAC    ENSG00000114771     AADAC
## AADACL2  ENSG00000197953   AADACL2

We add the same columns as in metadata :

row_oi = (sample_info$project_name == sample_name)

sobj$project_name = sample_name
sobj$sample_identifier = sample_info[row_oi, "sample_identifier"]
sobj$sample_type = sample_info[row_oi, "sample_type"]
sobj$location = sample_info[row_oi, "location"]
sobj$laboratory = sample_info[row_oi, "laboratory"]

colnames(sobj@meta.data)

## [1] "orig.ident"        "nCount_RNA"        "nFeature_RNA"     
## [4] "project_name"      "sample_identifier" "sample_type"      
## [7] "location"          "laboratory"

Before filtering

Normalization

sobj = Seurat::NormalizeData(sobj,
                             normalization.method = "LogNormalize",
                             assay = "RNA")

sobj = Seurat::FindVariableFeatures(sobj,
                                    assay = "RNA",
                                    nfeatures = 3000)
sobj

## An object of class Seurat 
## 14170 features across 3000 samples within 1 assay 
## Active assay: RNA (14170 features, 3000 variable features)

Projection

We generate a UMAP to visualize cells before filtering.

sobj = aquarius::dimensions_reduction(sobj = sobj,
                                      assay = "RNA",
                                      reduction = "pca",
                                      max_dims = 50,
                                      verbose = FALSE)
Seurat::ElbowPlot(sobj, ndims = 50, reduction = "RNA_pca")

We generate a UMAP with 20 principal components :

ndims = 20
sobj = Seurat::RunUMAP(sobj,
                       reduction = "RNA_pca",
                       dims = 1:ndims,
                       seed.use = 1337L,
                       reduction.name = paste0("RNA_pca_", ndims, "_umap"))

sobj

## An object of class Seurat 
## 14170 features across 3000 samples within 1 assay 
## Active assay: RNA (14170 features, 3000 variable features)
##  2 dimensional reductions calculated: RNA_pca, RNA_pca_20_umap

Cell type

We annotate cells for cell type using Seurat::AddModuleScore function.

sobj = aquarius::cell_annot_custom(sobj,
                                   newname = "cell_type",
                                   markers = cell_markers,
                                   use_negative = TRUE,
                                   add_score = TRUE,
                                   verbose = TRUE)

colnames(sobj@meta.data) = stringr::str_replace_all(string = colnames(sobj@meta.data),
                                                    pattern = " ",
                                                    replacement = "_")

sobj$cell_type = factor(sobj$cell_type, levels = names(cell_markers))

table(sobj$cell_type)

## 
##          CD4 T cells          CD8 T cells     Langerhans cells 
##                   19                  107                   63 
##          macrophages              B cells              cuticle 
##                   83                   92                  210 
##               cortex              medulla                  IRS 
##                  396                  168                  426 
##        proliferative               HF-SCs            IFE basal 
##                  165                  225                  173 
## IFE granular spinous                  ORS          melanocytes 
##                  445                  268                   77 
##            sebocytes 
##                   83

(Time to run : 1.8 s)

To justify cell type annotation, we can make a dotplot :

markers = c("PTPRC", "MSX2", "KRT16",
            unique(unlist(dotplot_markers[levels(sobj$cell_type)])))
markers = markers[markers %in% rownames(sobj)]

aquarius::plot_dotplot(sobj, assay = "RNA",
                       column_name = "cell_type",
                       markers = markers,
                       nb_hline = 0) +
  ggplot2::scale_color_gradientn(colors = aquarius:::color_gene) +
  ggplot2::theme(legend.position = "right",
                 legend.box = "vertical",
                 legend.direction = "vertical",
                 axis.title = element_blank(),
                 axis.text = element_text(size = 15))

We can make a barplot to see the composition of each dataset, and visualize cell types on the projection.

df_proportion = as.data.frame(prop.table(table(sobj$orig.ident,
                                               sobj$cell_type)))
colnames(df_proportion) = c("orig.ident", "cell_type", "freq")

quantif = table(sobj$orig.ident) %>%
  as.data.frame.table() %>%
  `colnames<-`(c("orig.ident", "nb_cells"))

# Plot
plot_list = list()

plot_list[[2]] = aquarius::plot_barplot(df = df_proportion,
                                        x = "orig.ident",
                                        y = "freq",
                                        fill = "cell_type",
                                        position = ggplot2::position_fill()) +
  ggplot2::scale_fill_manual(name = "Cell type",
                             values = color_markers[levels(df_proportion$cell_type)],
                             breaks = levels(df_proportion$cell_type)) +
  ggplot2::geom_label(data = quantif, inherit.aes = FALSE,
                      aes(x = orig.ident, y = 1.05, label = nb_cells),
                      label.size = 0)

plot_list[[1]] = Seurat::DimPlot(sobj, group.by = "cell_type") +
  ggplot2::scale_color_manual(values = unlist(color_markers),
                              breaks = names(color_markers)) +
  ggplot2::labs(title = sample_name,
                subtitle = paste0(ncol(sobj), " cells")) +
  Seurat::NoLegend() + Seurat::NoAxes() +
  ggplot2::theme(aspect.ratio = 1,
                 plot.title = element_text(hjust = 0.5),
                 plot.subtitle = element_text(hjust = 0.5))

patchwork::wrap_plots(plot_list, nrow = 1, widths = c(6, 1))

Cell cycle phase

We annotate cells for cell cycle phase using Seurat and cyclone.

cc_columns = aquarius::add_cell_cycle(sobj = sobj,
                                      assay = "RNA",
                                      species_rdx = "hs",
                                      BPPARAM = cl)@meta.data[, c("Seurat.Phase", "Phase")]

## 
##   G1  G2M    S 
## 1216  654  383

sobj$Seurat.Phase = cc_columns$Seurat.Phase
sobj$cyclone.Phase = cc_columns$Phase

table(sobj$Seurat.Phase, sobj$cyclone.Phase)

##            
##              G1 G2M   S
##   G1        797 419 265
##   G2M       157 146  41
##   S         262  89  77
##   Undecided   0   0   0

(Time to run : 110.02 s)

We visualize cell cycle on the projection :

plot_list = list()

plot_list[[2]] = Seurat::DimPlot(sobj, group.by = "Seurat.Phase") +
  ggplot2::labs(title = "Cell Cycle Phase",
                subtitle = "Seurat.Phase") +
  Seurat::NoLegend() + Seurat::NoAxes() +
  ggplot2::theme(aspect.ratio = 1,
                 plot.title = element_text(hjust = 0.5),
                 plot.subtitle = element_text(hjust = 0.5))

plot_list[[1]] = Seurat::DimPlot(sobj, group.by = "cyclone.Phase") +
  ggplot2::labs(title = "Cell Cycle Phase",
                subtitle = "cyclone.Phase") +
  Seurat::NoLegend() + Seurat::NoAxes() +
  ggplot2::theme(aspect.ratio = 1,
                 plot.title = element_text(hjust = 0.5),
                 plot.subtitle = element_text(hjust = 0.5))

patchwork::wrap_plots(plot_list, nrow = 1)

Quality control

In this section, we look at the number of genes expressed by each cell, the number of UMI, the percentage of mitochondrial genes expressed, and the percentage of ribosomal genes expressed.

We compute four quality metrics :

sobj = Seurat::PercentageFeatureSet(sobj, pattern = "^MT", col.name = "percent.mt")
sobj = Seurat::PercentageFeatureSet(sobj, pattern = "^RP[L|S][0-9]*$", col.name = "percent.rb")
sobj$log_nCount_RNA = log(sobj$nCount_RNA)

head(sobj@meta.data)

##              orig.ident nCount_RNA nFeature_RNA project_name sample_identifier
## ACCGTTCACTAC GSM3717036      18096         2931   GSM3717036    Takahashi_HD_3
## CTAATAGTTTGA GSM3717036       9759         2632   GSM3717036    Takahashi_HD_3
## ATAGCATGCACC GSM3717036       8860         2219   GSM3717036    Takahashi_HD_3
## AGCCCCATTTAG GSM3717036       6315         1715   GSM3717036    Takahashi_HD_3
## GCAGTCTACCAT GSM3717036       7219         1799   GSM3717036    Takahashi_HD_3
## ATTCGACCAAGG GSM3717036       6019         1915   GSM3717036    Takahashi_HD_3
##              sample_type   location laboratory score_CD4_T_cells
## ACCGTTCACTAC          HD hair scalp  Takahashi       -0.03173062
## CTAATAGTTTGA          HD hair scalp  Takahashi       -0.03901287
## ATAGCATGCACC          HD hair scalp  Takahashi       -0.02660790
## AGCCCCATTTAG          HD hair scalp  Takahashi       -0.01639574
## GCAGTCTACCAT          HD hair scalp  Takahashi       -0.02301986
## ATTCGACCAAGG          HD hair scalp  Takahashi       -0.03194420
##              score_CD8_T_cells score_Langerhans_cells score_macrophages
## ACCGTTCACTAC       -0.02517956            -0.03706621       -0.02696882
## CTAATAGTTTGA       -0.03130051            -0.06178143       -0.04516957
## ATAGCATGCACC       -0.01539585            -0.03819082       -0.02688366
## AGCCCCATTTAG       -0.01658928            -0.03313708       -0.01766800
## GCAGTCTACCAT       -0.02016997            -0.04386187       -0.02501728
## ATTCGACCAAGG       -0.02564684             0.17986723        0.06888658
##              score_B_cells score_cuticle score_cortex score_medulla  score_IRS
## ACCGTTCACTAC   -0.04885937    -0.1568707   0.04728849   -0.12458519 -0.2172633
## CTAATAGTTTGA   -0.04369022    -0.4161303  -0.22339344    0.03208894 -0.4146297
## ATAGCATGCACC   -0.01904630     0.4169276  -0.04715712    0.09942023  0.4438775
## AGCCCCATTTAG   -0.02374051    -0.3587425  -0.14403075   -0.22962979 -0.4963482
## GCAGTCTACCAT   -0.01448828    -0.3065465  -0.34131616   -0.12198573 -0.1098497
## ATTCGACCAAGG   -0.02445677    -0.3577165  -0.30537207   -0.02551720 -0.1824975
##              score_proliferative score_HF-SCs score_IFE_basal
## ACCGTTCACTAC         -0.10280283   -0.1512609      -0.1439294
## CTAATAGTTTGA         -0.11784224   -0.1324589      -0.4527119
## ATAGCATGCACC         -0.07493882   -0.2269830      -0.4211259
## AGCCCCATTTAG         -0.09823062   -0.3938491      -0.2336014
## GCAGTCTACCAT         -0.10514026   -0.2656295      -0.1401280
## ATTCGACCAAGG         -0.15432357   -0.0125482      -0.2495967
##              score_IFE_granular_spinous  score_ORS score_melanocytes
## ACCGTTCACTAC                -0.24809709 -0.3564199       -0.11506010
## CTAATAGTTTGA                -0.33222371  0.3465121        0.05130075
## ATAGCATGCACC                -0.56692919 -0.2945117       -0.34625640
## AGCCCCATTTAG                 0.97725701  0.0233339       -0.21412652
## GCAGTCTACCAT                 0.86454853 -0.1219940       -0.33200143
## ATTCGACCAAGG                 0.02576955  0.6104269       -0.07127572
##              score_sebocytes            cell_type Seurat.Phase cyclone.Phase
## ACCGTTCACTAC     -0.14717899               cortex           G1            G1
## CTAATAGTTTGA      0.11171118                  ORS           G1            G1
## ATAGCATGCACC     -0.05843992              cuticle            S            G1
## AGCCCCATTTAG     -0.18315066 IFE granular spinous           G1            G1
## GCAGTCTACCAT     -0.01954408 IFE granular spinous           G1            G1
## ATTCGACCAAGG      0.04424119                  ORS           G1            G1
##              percent.mt percent.rb log_nCount_RNA
## ACCGTTCACTAC   2.193855   7.222591       9.803446
## CTAATAGTTTGA   1.977662  14.284250       9.185945
## ATAGCATGCACC   2.155756  23.735892       9.089302
## AGCCCCATTTAG   1.662708  11.068884       8.750683
## GCAGTCTACCAT   3.227594  17.066076       8.884472
## ATTCGACCAAGG   1.063300  10.898820       8.702676

We get the cell barcodes for the failing cells :

fail_percent.mt = sobj@meta.data %>% dplyr::filter(percent.mt > cut_percent.mt) %>% rownames()
fail_percent.rb = sobj@meta.data %>% dplyr::filter(percent.rb > cut_percent.rb) %>% rownames()
fail_log_nCount_RNA = sobj@meta.data %>% dplyr::filter(log_nCount_RNA < cut_log_nCount_RNA) %>% rownames()
fail_nFeature_RNA = sobj@meta.data %>% dplyr::filter(nFeature_RNA < cut_nFeature_RNA) %>% rownames()

Quality control representation

We can visualize the 4 cells quality with a Venn diagram :

n_filtered = c(fail_percent.mt, fail_percent.rb, fail_log_nCount_RNA, fail_nFeature_RNA) %>%
  unique() %>% length()
percent_filtered = round(100*(n_filtered/ncol(sobj)), 2)

ggvenn::ggvenn(list(percent.mt = fail_percent.mt,
                    percent.rb = fail_percent.rb,
                    log_nCount_RNA = fail_log_nCount_RNA,
                    nFeature_RNA = fail_nFeature_RNA), 
               fill_color = c("#0073C2FF", "#EFC000FF", "orange", "pink"),
               stroke_size = 0.5, set_name_size = 4) +
  ggplot2::labs(title = "Filtered out cells",
                subtitle = paste0(n_filtered, " cells (", percent_filtered, " % of all cells)")) +
  ggplot2::theme(plot.title = element_text(hjust = 0.5, face = "bold"),
                 plot.subtitle = element_text(hjust = 0.5))

Number of UMI

To visualize the threshold for number of UMI, we can make a histogram :

aquarius::plot_qc_density(df = sobj@meta.data,
                          x = "log_nCount_RNA",
                          bins = 200,
                          group_by = "orig.ident",
                          group_color = setNames(sample_info$color,
                                                 nm = sample_info$sample_identifiant),
                          x_thresh = cut_log_nCount_RNA)

Seurat::VlnPlot(sobj, features = "log_nCount_RNA", pt.size = 0.001,
                group.by = "cell_type", cols = color_markers) +
  ggplot2::scale_fill_manual(values = color_markers, breaks = names(color_markers)) +
  ggplot2::geom_hline(yintercept = cut_log_nCount_RNA, col = "red") +
  ggplot2::labs(x = "")

sobj$fail = ifelse(colnames(sobj) %in% fail_log_nCount_RNA,
                   yes = as.character(sobj$cell_type), no = NA)
sobj$fail = factor(sobj$fail, levels = c(levels(sobj$cell_type), NA))

Seurat::DimPlot(sobj, group.by = "fail", na.value = "gray80", cols = color_markers) +
  ggplot2::labs(title = "log_nCount_RNA",
                subtitle = paste0(length(fail_log_nCount_RNA), " cells")) +
  Seurat::NoAxes() +
  ggplot2::theme(aspect.ratio = 1,
                 plot.title = element_text(hjust = 0.5),
                 plot.subtitle = element_text(hjust = 0.5))

Number of features

To visualize the threshold for number of features, we can make a histogram :

aquarius::plot_qc_density(df = sobj@meta.data,
                          x = "nFeature_RNA",
                          bins = 200,
                          group_by = "orig.ident",
                          group_color = setNames(sample_info$color,
                                                 nm = sample_info$sample_identifiant),
                          x_thresh = cut_nFeature_RNA)

Seurat::VlnPlot(sobj, features = "nFeature_RNA", pt.size = 0.001,
                group.by = "cell_type", cols = color_markers) +
  ggplot2::scale_fill_manual(values = color_markers, breaks = names(color_markers)) +
  ggplot2::geom_hline(yintercept = cut_nFeature_RNA, col = "red") +
  ggplot2::labs(x = "")

sobj$fail = ifelse(colnames(sobj) %in% fail_nFeature_RNA,
                   yes = as.character(sobj$cell_type), no = NA)
sobj$fail = factor(sobj$fail, levels = c(levels(sobj$cell_type), NA))

Seurat::DimPlot(sobj, group.by = "fail", na.value = "gray80", cols = color_markers) +
  ggplot2::labs(title = "nFeature_RNA",
                subtitle = paste0(length(fail_nFeature_RNA), " cells")) +
  Seurat::NoAxes() +
  ggplot2::theme(aspect.ratio = 1,
                 plot.title = element_text(hjust = 0.5),
                 plot.subtitle = element_text(hjust = 0.5))

Mitochondrial genes expression

To identify a threshold for mitochondrial gene expression, we can make a histogram :

aquarius::plot_qc_density(df = sobj@meta.data,
                          x = "percent.mt",
                          bins = 200,
                          group_by = "orig.ident",
                          group_color = setNames(sample_info$color,
                                                 nm = sample_info$sample_identifiant),
                          x_thresh = cut_percent.mt)

Seurat::VlnPlot(sobj, features = "percent.mt", pt.size = 0.001,
                group.by = "cell_type", cols = color_markers) +
  ggplot2::scale_fill_manual(values = color_markers, breaks = names(color_markers)) +
  ggplot2::geom_hline(yintercept = cut_percent.mt, col = "red") +
  ggplot2::labs(x = "")

sobj$fail = ifelse(colnames(sobj) %in% fail_percent.mt,
                   yes = as.character(sobj$cell_type), no = NA)
sobj$fail = factor(sobj$fail, levels = c(levels(sobj$cell_type), NA))

Seurat::DimPlot(sobj, group.by = "fail", na.value = "gray80", cols = color_markers) +
  ggplot2::labs(title = "percent.mt",
                subtitle = paste0(length(fail_percent.mt), " cells")) +
  Seurat::NoAxes() +
  ggplot2::theme(aspect.ratio = 1,
                 plot.title = element_text(hjust = 0.5),
                 plot.subtitle = element_text(hjust = 0.5))

Ribosomal genes expression

To identify a threshold for ribosomal gene expression, we can make a histogram :

aquarius::plot_qc_density(df = sobj@meta.data,
                          x = "percent.rb",
                          bins = 200,
                          group_by = "orig.ident",
                          group_color = setNames(sample_info$color,
                                                 nm = sample_info$sample_identifiant),
                          x_thresh = cut_percent.rb)

Seurat::VlnPlot(sobj, features = "percent.rb", pt.size = 0.001,
                group.by = "cell_type", cols = color_markers) +
  ggplot2::scale_fill_manual(values = color_markers, breaks = names(color_markers)) +
  ggplot2::geom_hline(yintercept = cut_percent.rb, col = "red") +
  ggplot2::labs(x = "")

sobj$fail = ifelse(colnames(sobj) %in% fail_percent.rb,
                   yes = as.character(sobj$cell_type), no = NA)
sobj$fail = factor(sobj$fail, levels = c(levels(sobj$cell_type), NA))

Seurat::DimPlot(sobj, group.by = "fail", na.value = "gray80", cols = color_markers) +
  ggplot2::labs(title = "percent.rb",
                subtitle = paste0(length(fail_percent.rb), " cells")) +
  Seurat::NoAxes() +
  ggplot2::theme(aspect.ratio = 1,
                 plot.title = element_text(hjust = 0.5),
                 plot.subtitle = element_text(hjust = 0.5))

FACS-like figure

We would like to see if the number of feature expressed by cell, and the number of UMI is correlated with the cell type, the percentage of mitochondrial and ribosomal gene expressed. We build the log_nCount_RNA by nFeature_RNA figure, where cells (dots) are colored by these different metrics.

This is the figure, colored by cell type :

aquarius::plot_qc_facslike(df = sobj@meta.data,
                           x = "nFeature_RNA",
                           y = "log_nCount_RNA",
                           col_by = "cell_type",
                           col_colors = unname(color_markers),
                           x_thresh = cut_nFeature_RNA,
                           y_thresh = cut_log_nCount_RNA,
                           bins = 200)

This is the figure, colored by the percentage of mitochondrial genes expressed in cell :

aquarius::plot_qc_facslike(df = sobj@meta.data,
                           x = "nFeature_RNA",
                           y = "log_nCount_RNA",
                           col_by = "percent.mt",
                           x_thresh = cut_nFeature_RNA,
                           y_thresh = cut_log_nCount_RNA,
                           bins = 200)

This is the figure, colored by the percentage of ribosomal genes expressed in cell :

aquarius::plot_qc_facslike(df = sobj@meta.data,
                           x = "nFeature_RNA",
                           y = "log_nCount_RNA",
                           col_by = "percent.rb",
                           x_thresh = cut_nFeature_RNA,
                           y_thresh = cut_log_nCount_RNA,
                           bins = 200)

Visualization as piechart

Do filtered cells belong to a particular cell type ?

sobj$all_cells = TRUE

plot_list = list()

## All cells
df = sobj@meta.data
if (nrow(df) == 0) {
  plot_list[[1]] = ggplot()
} else {
  plot_list[[1]] = aquarius::plot_piechart(df = df,
                                           logical_var = "all_cells",
                                           grouping_var = "cell_type",
                                           colors = color_markers,
                                           display_legend = TRUE) +
    ggplot2::labs(title = "All cells",
                  subtitle = paste(nrow(df), "cells")) +
    ggplot2::theme(plot.title = element_text(hjust = 0.5, face = "bold"),
                   plot.subtitle = element_text(hjust = 0.5))
}

## Doublet cells: not done
plot_list[[2]] = ggplot()

## percent.mt
df = sobj@meta.data %>%
  dplyr::filter(percent.mt > cut_percent.mt)
if (nrow(df) == 0) {
  plot_list[[3]] = ggplot()
} else {
  plot_list[[3]] = aquarius::plot_piechart(df = df,
                                           logical_var = "all_cells",
                                           grouping_var = "cell_type",
                                           colors = color_markers,
                                           display_legend = TRUE) +
    ggplot2::labs(title = paste("percent.mt >", cut_percent.mt),
                  subtitle = paste(length(fail_percent.mt), "cells")) +
    ggplot2::theme(plot.title = element_text(hjust = 0.5, face = "bold"),
                   plot.subtitle = element_text(hjust = 0.5))
}

## percent.rb
df = sobj@meta.data %>%
  dplyr::filter(percent.rb > cut_percent.rb)
if (nrow(df) == 0) {
  plot_list[[4]] = ggplot()
} else {
  plot_list[[4]] = aquarius::plot_piechart(df = df,
                                           logical_var = "all_cells",
                                           grouping_var = "cell_type",
                                           colors = color_markers,
                                           display_legend = TRUE) +
    ggplot2::labs(title = paste("percent.rb >", cut_percent.rb),
                  subtitle = paste(length(fail_percent.rb), "cells")) +
    ggplot2::theme(plot.title = element_text(hjust = 0.5, face = "bold"),
                   plot.subtitle = element_text(hjust = 0.5))
}

## log_nCount_RNA
df = sobj@meta.data %>%
  dplyr::filter(log_nCount_RNA < cut_log_nCount_RNA)
if (nrow(df) == 0) {
  plot_list[[5]] = ggplot()
} else {
  plot_list[[5]] = aquarius::plot_piechart(df = df,
                                           logical_var = "all_cells",
                                           grouping_var = "cell_type",
                                           colors = color_markers,
                                           display_legend = TRUE) +
    ggplot2::labs(title = paste("log_nCount_RNA <", round(cut_log_nCount_RNA, 2)),
                  subtitle = paste(length(fail_log_nCount_RNA), "cells")) +
    ggplot2::theme(plot.title = element_text(hjust = 0.5, face = "bold"),
                   plot.subtitle = element_text(hjust = 0.5))
}

## nFeature_RNA
df = sobj@meta.data %>%
  dplyr::filter(nFeature_RNA < cut_nFeature_RNA)
if (nrow(df) == 0) {
  plot_list[[6]] = ggplot()
} else {
  plot_list[[6]] = aquarius::plot_piechart(df = df,
                                           logical_var = "all_cells",
                                           grouping_var = "cell_type",
                                           colors = color_markers,
                                           display_legend = TRUE) +
    ggplot2::labs(title = paste("nFeature_RNA <", round(cut_nFeature_RNA, 2)),
                  subtitle = paste(length(fail_nFeature_RNA), "cells")) +
    ggplot2::theme(plot.title = element_text(hjust = 0.5, face = "bold"),
                   plot.subtitle = element_text(hjust = 0.5))
}

patchwork::wrap_plots(plot_list, ncol = 3) +
  patchwork::plot_layout(guides = "collect") &
  ggplot2::theme(legend.position = "right")

Save

We could save this object before filtering (remove eval = FALSE) :

saveRDS(sobj, paste0(out_dir, "/datasets/", sample_name, "_sobj_unfiltered.rds"))

Filtering

We remove :

• cells with a number of UMI lower than 0.5
• cells expressing a number of genes lower than 250
• cells having more than 20 % of UMI related to mitochondrial genes
• cells having more than 50 % of UMI related to ribosomal genes

Note: We do not filter cells detected as doublets. Indeed, few genes and transcripts are detected per cell, and the best cells are therefore annotated as doublets.

sobj = subset(sobj, invert = TRUE,
              cells = unique(c(fail_log_nCount_RNA, fail_nFeature_RNA,
                               fail_percent.mt, fail_percent.rb)))
sobj

## An object of class Seurat 
## 14170 features across 510 samples within 1 assay 
## Active assay: RNA (14170 features, 3000 variable features)
##  2 dimensional reductions calculated: RNA_pca, RNA_pca_20_umap

Post-filtering processing

Normalization

We normalize the count matrix for remaining cells :

sobj = Seurat::NormalizeData(sobj,
                             normalization.method = "LogNormalize",
                             assay = "RNA")

sobj = Seurat::FindVariableFeatures(sobj,
                                    assay = "RNA",
                                    nfeatures = 3000)
sobj

## An object of class Seurat 
## 14170 features across 510 samples within 1 assay 
## Active assay: RNA (14170 features, 3000 variable features)
##  2 dimensional reductions calculated: RNA_pca, RNA_pca_20_umap

Projection

We perform a PCA :

sobj = aquarius::dimensions_reduction(sobj = sobj,
                                      assay = "RNA",
                                      reduction = "pca",
                                      max_dims = 50,
                                      verbose = FALSE)
Seurat::ElbowPlot(sobj, ndims = 50, reduction = "RNA_pca")

We generate a UMAP with 20 principal components :

ndims = 20
sobj = Seurat::RunUMAP(sobj,
                       reduction = "RNA_pca",
                       dims = 1:ndims,
                       seed.use = 1337L,
                       reduction.name = paste0("RNA_pca_", ndims, "_umap"))

Annotation

We annotate cells for cell type, with the new normalized expression matrix :

score_columns = grep(x = colnames(sobj@meta.data), pattern = "^score", value = TRUE)
sobj@meta.data[, score_columns] = NULL
sobj$cell_type = NULL

sobj = aquarius::cell_annot_custom(sobj,
                                   newname = "cell_type",
                                   markers = cell_markers,
                                   use_negative = TRUE,
                                   add_score = TRUE,
                                   verbose = TRUE)

sobj$cell_type = factor(sobj$cell_type, levels = names(cell_markers))

colnames(sobj@meta.data) = stringr::str_replace_all(string = colnames(sobj@meta.data),
                                                    pattern = " ",
                                                    replacement = "_")

table(sobj$cell_type)

## 
##          CD4 T cells          CD8 T cells     Langerhans cells 
##                    2                    2                    3 
##          macrophages              B cells              cuticle 
##                    3                    9                   46 
##               cortex              medulla                  IRS 
##                   35                   15                   40 
##        proliferative               HF-SCs            IFE basal 
##                   26                   65                   42 
## IFE granular spinous                  ORS          melanocytes 
##                  123                   67                   13 
##            sebocytes 
##                   19

(Time to run : 1.69 s)

To justify cell type annotation, we can make a dotplot :

markers = c("PTPRC", unique(unlist(dotplot_markers[levels(sobj$cell_type)])))
markers = markers[markers %in% rownames(sobj)]

aquarius::plot_dotplot(sobj, assay = "RNA",
                       column_name = "cell_type",
                       markers = markers,
                       nb_hline = 0) +
  ggplot2::scale_color_gradientn(colors = aquarius:::color_gene) +
  ggplot2::theme(legend.position = "right",
                 legend.box = "vertical",
                 legend.direction = "vertical",
                 axis.title = element_blank(),
                 axis.text = element_text(size = 15))

We can make a barplot to see the composition of each dataset, and visualize cell types on the projection.

df_proportion = as.data.frame(prop.table(table(sobj$orig.ident,
                                               sobj$cell_type)))
colnames(df_proportion) = c("orig.ident", "cell_type", "freq")

quantif = table(sobj$orig.ident) %>%
  as.data.frame.table() %>%
  `colnames<-`(c("orig.ident", "nb_cells"))

# Plot
plot_list = list()

plot_list[[2]] = aquarius::plot_barplot(df = df_proportion,
                                        x = "orig.ident",
                                        y = "freq",
                                        fill = "cell_type",
                                        position = ggplot2::position_fill()) +
  ggplot2::scale_fill_manual(name = "Cell type",
                             values = color_markers[levels(df_proportion$cell_type)],
                             breaks = levels(df_proportion$cell_type)) +
  ggplot2::geom_label(data = quantif, inherit.aes = FALSE,
                      aes(x = orig.ident, y = 1.05, label = nb_cells),
                      label.size = 0)

plot_list[[1]] = Seurat::DimPlot(sobj, group.by = "cell_type",
                                 reduction = "RNA_pca_20_umap") +
  ggplot2::scale_color_manual(values = unlist(color_markers),
                              breaks = names(color_markers)) +
  ggplot2::labs(title = sample_name,
                subtitle = paste0(ncol(sobj), " cells")) +
  Seurat::NoLegend() + Seurat::NoAxes() +
  ggplot2::theme(aspect.ratio = 1,
                 plot.title = element_text(hjust = 0.5),
                 plot.subtitle = element_text(hjust = 0.5))

patchwork::wrap_plots(plot_list, nrow = 1, widths = c(6, 1))

Cell cycle

We annotate cells for cell cycle phase :

cc_columns = aquarius::add_cell_cycle(sobj = sobj,
                                      assay = "RNA",
                                      species_rdx = "hs",
                                      BPPARAM = cl)@meta.data[, c("Seurat.Phase", "Phase")]

## 
##  G1 G2M   S 
## 402  53  55

sobj$Seurat.Phase = cc_columns$Seurat.Phase
sobj$cyclone.Phase = cc_columns$Phase

table(sobj$Seurat.Phase, sobj$cyclone.Phase)

##      
##        G1 G2M   S
##   G1  187  25  29
##   G2M 106  18  14
##   S   109  10  12

(Time to run : 29.27 s)

We visualize cell cycle on the projection :

plot_list = list()

plot_list[[2]] = Seurat::DimPlot(sobj, group.by = "Seurat.Phase",
                                 reduction = "RNA_pca_20_umap") +
  ggplot2::labs(title = "Cell Cycle Phase",
                subtitle = "Seurat.Phase") +
  Seurat::NoLegend() + Seurat::NoAxes() +
  ggplot2::theme(aspect.ratio = 1,
                 plot.title = element_text(hjust = 0.5),
                 plot.subtitle = element_text(hjust = 0.5))

plot_list[[1]] = Seurat::DimPlot(sobj, group.by = "cyclone.Phase",
                                 reduction = "RNA_pca_20_umap") +
  ggplot2::labs(title = "Cell Cycle Phase",
                subtitle = "cyclone.Phase") +
  Seurat::NoLegend() + Seurat::NoAxes() +
  ggplot2::theme(aspect.ratio = 1,
                 plot.title = element_text(hjust = 0.5),
                 plot.subtitle = element_text(hjust = 0.5))

patchwork::wrap_plots(plot_list, nrow = 1)

Clustering

We make a highly resolutive clustering :

sobj = Seurat::FindNeighbors(sobj, reduction = "RNA_pca", dims = c(1:ndims))
sobj = Seurat::FindClusters(sobj, resolution = 2)

## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 510
## Number of edges: 17622
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.4912
## Number of communities: 10
## Elapsed time: 0 seconds

table(sobj$seurat_clusters)

## 
##  0  1  2  3  4  5  6  7  8  9 
## 83 70 69 55 53 46 45 44 25 20

Visualization

Cell type

We can visualize the cell type :

Seurat::DimPlot(sobj, group.by = "cell_type",
                reduction = paste0("RNA_pca_", ndims, "_umap"), cols = color_markers) +
  Seurat::NoAxes() + ggplot2::ggtitle("UMAP") +
  ggplot2::theme(aspect.ratio = 1,
                 plot.title = element_text(hjust = 0.5))

Cell cycle

We can visualize the cell cycle, from Seurat :

Seurat::DimPlot(sobj, group.by = "Seurat.Phase",
                reduction = paste0("RNA_pca_", ndims, "_umap")) +
  Seurat::NoAxes() + ggplot2::ggtitle("UMAP") +
  ggplot2::theme(aspect.ratio = 1,
                 plot.title = element_text(hjust = 0.5))

We can visualize the cell cycle, from cyclone :

Seurat::DimPlot(sobj, group.by = "cyclone.Phase",
                reduction = paste0("RNA_pca_", ndims, "_umap")) +
  Seurat::NoAxes() + ggplot2::ggtitle("UMAP") +
  ggplot2::theme(aspect.ratio = 1,
                 plot.title = element_text(hjust = 0.5))

Clusters

We visualize the clustering :

Seurat::DimPlot(sobj, group.by = "seurat_clusters", label = TRUE,
                reduction = paste0("RNA_pca_", ndims, "_umap")) +
  Seurat::NoAxes() + ggplot2::ggtitle("UMAP") +
  ggplot2::theme(aspect.ratio = 1,
                 plot.title = element_text(hjust = 0.5))

Gene expression

We visualize all cell types markers on the UMAP :

markers = dotplot_markers %>% unlist() %>% unname()
markers = markers[markers %in% rownames(sobj)]

plot_list = lapply(markers,
                   FUN = function(one_gene) {
                     p = Seurat::FeaturePlot(sobj, features = one_gene,
                                             reduction = paste0("RNA_pca_", ndims, "_umap")) +
                       ggplot2::labs(title = one_gene) +
                       ggplot2::scale_color_gradientn(colors = aquarius::color_gene) +
                       ggplot2::theme(aspect.ratio = 1,
                                      plot.subtitle = element_text(hjust = 0.5)) +
                       Seurat::NoAxes()
                     return(p)
                   })

patchwork::wrap_plots(plot_list, ncol = 4)

Save

We save the annotated and filtered Seurat object :

saveRDS(sobj, file = paste0(out_dir, "/datasets/", sample_name, "_sobj_filtered.rds"))

R session

show

## R version 3.6.3 (2020-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.6 LTS
## 
## Matrix products: default
## BLAS:   /usr/local/lib/R/lib/libRblas.so
## LAPACK: /usr/local/lib/R/lib/libRlapack.so
## 
## locale:
## [1] C
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] ggplot2_3.3.5   patchwork_1.1.2 dplyr_1.0.7    
## 
## loaded via a namespace (and not attached):
##   [1] softImpute_1.4              graphlayouts_0.7.0         
##   [3] pbapply_1.4-2               lattice_0.20-41            
##   [5] haven_2.3.1                 vctrs_0.3.8                
##   [7] usethis_2.0.1               dynwrap_1.2.1              
##   [9] blob_1.2.1                  survival_3.2-13            
##  [11] prodlim_2019.11.13          dynutils_1.0.5             
##  [13] later_1.3.0                 DBI_1.1.1                  
##  [15] R.utils_2.11.0              SingleCellExperiment_1.8.0 
##  [17] rappdirs_0.3.3              uwot_0.1.8                 
##  [19] dqrng_0.2.1                 jpeg_0.1-8.1               
##  [21] zlibbioc_1.32.0             pspline_1.0-18             
##  [23] pcaMethods_1.78.0           mvtnorm_1.1-1              
##  [25] htmlwidgets_1.5.4           GlobalOptions_0.1.2        
##  [27] future_1.22.1               UpSetR_1.4.0               
##  [29] laeken_0.5.2                leiden_0.3.3               
##  [31] clustree_0.4.3              parallel_3.6.3             
##  [33] scater_1.14.6               irlba_2.3.3                
##  [35] DEoptimR_1.0-9              tidygraph_1.1.2            
##  [37] Rcpp_1.0.9                  readr_2.0.2                
##  [39] KernSmooth_2.23-17          carrier_0.1.0              
##  [41] promises_1.1.0              gdata_2.18.0               
##  [43] DelayedArray_0.12.3         limma_3.42.2               
##  [45] graph_1.64.0                RcppParallel_5.1.4         
##  [47] Hmisc_4.4-0                 fs_1.5.2                   
##  [49] RSpectra_0.16-0             fastmatch_1.1-0            
##  [51] ranger_0.12.1               digest_0.6.25              
##  [53] png_0.1-7                   sctransform_0.2.1          
##  [55] cowplot_1.0.0               DOSE_3.12.0                
##  [57] ggvenn_0.1.9                here_1.0.1                 
##  [59] TInGa_0.0.0.9000            ggraph_2.0.3               
##  [61] pkgconfig_2.0.3             GO.db_3.10.0               
##  [63] DelayedMatrixStats_1.8.0    gower_0.2.1                
##  [65] ggbeeswarm_0.6.0            iterators_1.0.12           
##  [67] DropletUtils_1.6.1          reticulate_1.26            
##  [69] clusterProfiler_3.14.3      SummarizedExperiment_1.16.1
##  [71] circlize_0.4.15             beeswarm_0.4.0             
##  [73] GetoptLong_1.0.5            xfun_0.35                  
##  [75] bslib_0.3.1                 zoo_1.8-10                 
##  [77] tidyselect_1.1.0            reshape2_1.4.4             
##  [79] purrr_0.3.4                 ica_1.0-2                  
##  [81] pcaPP_1.9-73                viridisLite_0.3.0          
##  [83] rtracklayer_1.46.0          rlang_1.0.2                
##  [85] hexbin_1.28.1               jquerylib_0.1.4            
##  [87] dyneval_0.9.9               glue_1.4.2                 
##  [89] RColorBrewer_1.1-2          matrixStats_0.56.0         
##  [91] stringr_1.4.0               lava_1.6.7                 
##  [93] europepmc_0.3               DESeq2_1.26.0              
##  [95] recipes_0.1.17              labeling_0.3               
##  [97] httpuv_1.5.2                class_7.3-17               
##  [99] BiocNeighbors_1.4.2         DO.db_2.9                  
## [101] annotate_1.64.0             jsonlite_1.7.2             
## [103] XVector_0.26.0              bit_4.0.4                  
## [105] mime_0.9                    aquarius_0.1.5             
## [107] Rsamtools_2.2.3             gridExtra_2.3              
## [109] gplots_3.0.3                stringi_1.4.6              
## [111] processx_3.5.2              gsl_2.1-6                  
## [113] bitops_1.0-6                cli_3.0.1                  
## [115] batchelor_1.2.4             RSQLite_2.2.0              
## [117] randomForest_4.6-14         tidyr_1.1.4                
## [119] data.table_1.14.2           rstudioapi_0.13            
## [121] org.Mm.eg.db_3.10.0         GenomicAlignments_1.22.1   
## [123] nlme_3.1-147                qvalue_2.18.0              
## [125] scran_1.14.6                locfit_1.5-9.4             
## [127] scDblFinder_1.1.8           listenv_0.8.0              
## [129] ggthemes_4.2.4              gridGraphics_0.5-0         
## [131] R.oo_1.24.0                 dbplyr_1.4.4               
## [133] BiocGenerics_0.32.0         TTR_0.24.2                 
## [135] readxl_1.3.1                lifecycle_1.0.1            
## [137] timeDate_3043.102           ggpattern_0.3.1            
## [139] munsell_0.5.0               cellranger_1.1.0           
## [141] R.methodsS3_1.8.1           proxyC_0.1.5               
## [143] visNetwork_2.0.9            caTools_1.18.0             
## [145] codetools_0.2-16            Biobase_2.46.0             
## [147] GenomeInfoDb_1.22.1         vipor_0.4.5                
## [149] lmtest_0.9-38               msigdbr_7.5.1              
## [151] htmlTable_1.13.3            triebeard_0.3.0            
## [153] lsei_1.2-0                  xtable_1.8-4               
## [155] ROCR_1.0-7                  BiocManager_1.30.10        
## [157] scatterplot3d_0.3-41        abind_1.4-5                
## [159] farver_2.0.3                parallelly_1.28.1          
## [161] RANN_2.6.1                  askpass_1.1                
## [163] GenomicRanges_1.38.0        RcppAnnoy_0.0.16           
## [165] tibble_3.1.5                ggdendro_0.1-20            
## [167] cluster_2.1.0               future.apply_1.5.0         
## [169] Seurat_3.1.5                dendextend_1.15.1          
## [171] Matrix_1.3-2                ellipsis_0.3.2             
## [173] prettyunits_1.1.1           lubridate_1.7.9            
## [175] ggridges_0.5.2              igraph_1.2.5               
## [177] RcppEigen_0.3.3.7.0         fgsea_1.12.0               
## [179] remotes_2.4.2               scBFA_1.0.0                
## [181] destiny_3.0.1               VIM_6.1.1                  
## [183] testthat_3.1.0              htmltools_0.5.2            
## [185] BiocFileCache_1.10.2        yaml_2.2.1                 
## [187] utf8_1.1.4                  plotly_4.9.2.1             
## [189] XML_3.99-0.3                ModelMetrics_1.2.2.2       
## [191] e1071_1.7-3                 foreign_0.8-76             
## [193] withr_2.5.0                 fitdistrplus_1.0-14        
## [195] BiocParallel_1.20.1         xgboost_1.4.1.1            
## [197] bit64_4.0.5                 foreach_1.5.0              
## [199] robustbase_0.93-9           Biostrings_2.54.0          
## [201] GOSemSim_2.13.1             rsvd_1.0.3                 
## [203] memoise_2.0.0               evaluate_0.18              
## [205] forcats_0.5.0               rio_0.5.16                 
## [207] geneplotter_1.64.0          tzdb_0.1.2                 
## [209] caret_6.0-86                ps_1.6.0                   
## [211] DiagrammeR_1.0.6.1          curl_4.3                   
## [213] fdrtool_1.2.15              fansi_0.4.1                
## [215] highr_0.8                   urltools_1.7.3             
## [217] xts_0.12.1                  GSEABase_1.48.0            
## [219] acepack_1.4.1               edgeR_3.28.1               
## [221] checkmate_2.0.0             scds_1.2.0                 
## [223] cachem_1.0.6                npsurv_0.4-0               
## [225] babelgene_22.3              rjson_0.2.20               
## [227] openxlsx_4.1.5              ggrepel_0.9.1              
## [229] clue_0.3-60                 rprojroot_2.0.2            
## [231] stabledist_0.7-1            tools_3.6.3                
## [233] sass_0.4.0                  nichenetr_1.1.1            
## [235] magrittr_2.0.1              RCurl_1.98-1.2             
## [237] proxy_0.4-24                car_3.0-11                 
## [239] ape_5.3                     ggplotify_0.0.5            
## [241] xml2_1.3.2                  httr_1.4.2                 
## [243] assertthat_0.2.1            rmarkdown_2.18             
## [245] boot_1.3-25                 globals_0.14.0             
## [247] R6_2.4.1                    Rhdf5lib_1.8.0             
## [249] nnet_7.3-14                 RcppHNSW_0.2.0             
## [251] progress_1.2.2              genefilter_1.68.0          
## [253] statmod_1.4.34              gtools_3.8.2               
## [255] shape_1.4.6                 HDF5Array_1.14.4           
## [257] BiocSingular_1.2.2          rhdf5_2.30.1               
## [259] splines_3.6.3               AUCell_1.8.0               
## [261] carData_3.0-4               colorspace_1.4-1           
## [263] generics_0.1.0              stats4_3.6.3               
## [265] base64enc_0.1-3             dynfeature_1.0.0           
## [267] smoother_1.1                gridtext_0.1.1             
## [269] pillar_1.6.3                tweenr_1.0.1               
## [271] sp_1.4-1                    ggplot.multistats_1.0.0    
## [273] rvcheck_0.1.8               GenomeInfoDbData_1.2.2     
## [275] plyr_1.8.6                  gtable_0.3.0               
## [277] zip_2.2.0                   knitr_1.41                 
## [279] ComplexHeatmap_2.14.0       latticeExtra_0.6-29        
## [281] biomaRt_2.42.1              IRanges_2.20.2             
## [283] fastmap_1.1.0               ADGofTest_0.3              
## [285] copula_1.0-0                doParallel_1.0.15          
## [287] AnnotationDbi_1.48.0        vcd_1.4-8                  
## [289] babelwhale_1.0.1            openssl_1.4.1              
## [291] scales_1.1.1                backports_1.2.1            
## [293] S4Vectors_0.24.4            ipred_0.9-12               
## [295] enrichplot_1.6.1            hms_1.1.1                  
## [297] ggforce_0.3.1               Rtsne_0.15                 
## [299] shiny_1.7.1                 numDeriv_2016.8-1.1        
## [301] polyclip_1.10-0             grid_3.6.3                 
## [303] lazyeval_0.2.2              Formula_1.2-3              
## [305] tsne_0.1-3                  crayon_1.3.4               
## [307] MASS_7.3-54                 pROC_1.16.2                
## [309] viridis_0.5.1               dynparam_1.0.0             
## [311] rpart_4.1-15                zinbwave_1.8.0             
## [313] compiler_3.6.3              ggtext_0.1.0